Variant report

Variant	rs1473385
Chromosome Location	chr3:46920066-46920067
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr3:46919827-46920925	SK-N-SH	brain:	n/a	n/a
2	TFAP2C	chr3:46919982-46920914	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46917376..46920621-chr3:46922888..46926605,5	K562	blood:
2	chr3:46919067..46921668-chr3:46922191..46925334,3	K562	blood:
3	chr3:46917885..46923537-chr3:46925586..46931315,6	MCF-7	breast:
4	chr3:46707887..46708803-chr3:46920018..46920840,3	MCF-7	breast:

Variant related genes	Relation type
PTH1R	TF binding region
ENSG00000160801	Chromatin interaction
ENSG00000160808	Chromatin interaction
ENSG00000268537	Chromatin interaction

Extended variants
information (count: 154 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10461017	1.00[EUR][1000 genomes]
rs10461019	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11130108	1.00[EUR][1000 genomes]
rs11130109	1.00[EUR][1000 genomes]
rs11706212	1.00[EUR][1000 genomes]
rs11708257	1.00[EUR][1000 genomes]
rs11709693	1.00[EUR][1000 genomes]
rs11709876	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11713537	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs11928558	1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12487763	1.00[EUR][1000 genomes]
rs13062185	1.00[EUR][1000 genomes]
rs13079416	1.00[EUR][1000 genomes]
rs13082531	1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1378818	1.00[EUR][1000 genomes]
rs1463394	1.00[EUR][1000 genomes]
rs1466272	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1466273	1.00[EUR][1000 genomes]
rs1473382	1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1563431	1.00[EUR][1000 genomes]
rs1563432	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1814564	1.00[EUR][1000 genomes]
rs1869870	1.00[EUR][1000 genomes]
rs2124509	1.00[EUR][1000 genomes]
rs2168442	0.83[ASW][hapmap]
rs2385861	0.83[ASW][hapmap]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3930202	1.00[EUR][1000 genomes]
rs4018904	1.00[EUR][1000 genomes]
rs4282092	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4289375	1.00[EUR][1000 genomes]
rs4324490	1.00[EUR][1000 genomes]
rs4373094	1.00[EUR][1000 genomes]
rs4378998	1.00[EUR][1000 genomes]
rs4389512	1.00[EUR][1000 genomes]
rs4450857	1.00[EUR][1000 genomes]
rs4478107	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4519738	1.00[EUR][1000 genomes]
rs4522803	1.00[EUR][1000 genomes]
rs4525902	1.00[EUR][1000 genomes]
rs4543047	1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4682832	1.00[EUR][1000 genomes]
rs4682833	1.00[EUR][1000 genomes]
rs4682834	1.00[EUR][1000 genomes]
rs4682835	1.00[EUR][1000 genomes]
rs4682836	1.00[EUR][1000 genomes]
rs4682838	1.00[EUR][1000 genomes]
rs4682841	1.00[EUR][1000 genomes]
rs4682843	1.00[EUR][1000 genomes]
rs4682846	1.00[EUR][1000 genomes]
rs4682847	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683261	1.00[EUR][1000 genomes]
rs4683262	1.00[EUR][1000 genomes]
rs4683265	1.00[EUR][1000 genomes]
rs4683277	1.00[EUR][1000 genomes]
rs4683279	1.00[EUR][1000 genomes]
rs4683282	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4683283	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683284	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683285	1.00[EUR][1000 genomes]
rs4683286	1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	1.00[EUR][1000 genomes]
rs4683290	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683291	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683292	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683293	1.00[EUR][1000 genomes]
rs4683303	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442014	1.00[EUR][1000 genomes]
rs6442015	1.00[EUR][1000 genomes]
rs6442041	1.00[EUR][1000 genomes]
rs6442042	1.00[EUR][1000 genomes]
rs6442043	1.00[EUR][1000 genomes]
rs6442044	1.00[EUR][1000 genomes]
rs6442047	1.00[EUR][1000 genomes]
rs6442048	1.00[EUR][1000 genomes]
rs6766676	1.00[EUR][1000 genomes]
rs6768169	1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6780994	1.00[EUR][1000 genomes]
rs6785462	1.00[EUR][1000 genomes]
rs6804732	1.00[EUR][1000 genomes]
rs6806521	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6808052	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6809904	1.00[EUR][1000 genomes]
rs7621530	1.00[EUR][1000 genomes]
rs7624549	1.00[EUR][1000 genomes]
rs7630904	1.00[EUR][1000 genomes]
rs7638549	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7641494	1.00[EUR][1000 genomes]
rs7643868	1.00[EUR][1000 genomes]
rs7644382	1.00[EUR][1000 genomes]
rs7646076	1.00[EUR][1000 genomes]
rs7649941	1.00[EUR][1000 genomes]
rs7650142	1.00[EUR][1000 genomes]
rs7650245	1.00[EUR][1000 genomes]
rs936173	0.87[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936177	1.00[EUR][1000 genomes]
rs936178	1.00[EUR][1000 genomes]
rs936179	1.00[EUR][1000 genomes]
rs936180	1.00[EUR][1000 genomes]
rs936181	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs936182	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs936185	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs936186	1.00[EUR][1000 genomes]
rs939409	1.00[EUR][1000 genomes]
rs939410	1.00[EUR][1000 genomes]
rs939411	1.00[EUR][1000 genomes]
rs939412	1.00[EUR][1000 genomes]
rs939413	1.00[EUR][1000 genomes]
rs939415	1.00[EUR][1000 genomes]
rs939416	1.00[EUR][1000 genomes]
rs939417	1.00[EUR][1000 genomes]
rs939420	1.00[EUR][1000 genomes]
rs9810881	1.00[EUR][1000 genomes]
rs9812407	1.00[EUR][1000 genomes]
rs9819344	1.00[EUR][1000 genomes]
rs9819475	1.00[EUR][1000 genomes]
rs9823480	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9827293	1.00[EUR][1000 genomes]
rs9828473	1.00[EUR][1000 genomes]
rs9833500	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9836801	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9850151	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9862711	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]
rs9878813	1.00[EUR][1000 genomes]
rs9883152	1.00[EUR][1000 genomes]
rs9883909	1.00[EUR][1000 genomes]
rs9990284	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv590205	chr3:46852679-46929546	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv590206	chr3:46873957-46935527	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	esv3331463	chr3:46920033-46920257	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46912200-46921000	Enhancers	Fetal Heart	heart
2	chr3:46913600-46920200	Weak transcription	Pancreas	Pancrea
3	chr3:46914400-46921400	Enhancers	Fetal Intestine Large	intestine
4	chr3:46915400-46921600	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:46915800-46923000	Weak transcription	Brain Anterior Caudate	brain
6	chr3:46916000-46921600	Enhancers	Fetal Intestine Small	intestine
7	chr3:46916000-46922400	Weak transcription	Adipose Nuclei	Adipose
8	chr3:46916400-46920200	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:46916600-46920200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:46916800-46920200	Weak transcription	Lung	lung
11	chr3:46916800-46921000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:46917000-46922000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr3:46917000-46922800	Weak transcription	Ovary	ovary
14	chr3:46917200-46920200	Weak transcription	Right Ventricle	heart
15	chr3:46917200-46922800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:46917800-46921000	Enhancers	HSMM	muscle
17	chr3:46917800-46922600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr3:46918000-46920200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:46918000-46920800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:46918000-46921000	Enhancers	HSMMtube	muscle
21	chr3:46918000-46922400	Enhancers	Placenta	Placenta
22	chr3:46918200-46920400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:46918400-46920800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr3:46918600-46920200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:46918600-46921000	Enhancers	Fetal Lung	lung
26	chr3:46918800-46920800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:46918800-46920800	Enhancers	Stomach Smooth Muscle	stomach
28	chr3:46919200-46920200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:46919200-46920200	Bivalent Enhancer	HepG2	liver
30	chr3:46919200-46922200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:46919400-46920200	Enhancers	Fetal Muscle Leg	muscle
32	chr3:46919400-46921000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr3:46919600-46920200	Enhancers	Hela-S3	cervix
34	chr3:46919600-46920600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:46919600-46920600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:46919600-46920800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:46919600-46920800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:46919800-46920800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
39	chr3:46919800-46921200	Enhancers	A549	lung
40	chr3:46919800-46921400	Enhancers	Fetal Stomach	stomach
41	chr3:46920000-46920200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
42	chr3:46920000-46920400	Weak transcription	Fetal Kidney	kidney
43	chr3:46920000-46920600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:46920000-46920600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:46920000-46920600	Enhancers	Spleen	Spleen
46	chr3:46920000-46920600	Enhancers	HMEC	breast
47	chr3:46920000-46920800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
48	chr3:46920000-46920800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:46920000-46920800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:46920000-46920800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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